- <strong>Example RNAalifold Output</strong><br />
- RNAalifold prints a consensus alignment and mfe structure to stdout with its
- associated energy. Depending on the arguments given, other information such as
- alternate structures are displayed below while base pairing probabilities (-p or --MEA
- options) are stored in a separate 'alifold.out' file.<br />
- <pre><br />
-G_UUUCAUU___AUGACGGCCUGUGCU_UAAA__CCUCC____GAG__C________GGGUCA_G_G_UCUGAU___CUUG_______GAGAC
-(.((((...........(((((((((........(((......)))............))))).).).))..................))))) (-19.16 = -11.80 + -7.36)
-(.((((...........(((((((((........(((......)))............))))).).).))..................))))) [-19.32]
- frequency of mfe structure in ensemble 0.765639
-(.((((...........(((((((((........(((......)))............))))).).).))..................))))) -19.16 {-11.80 + -7.36}
-(.((((...........(((((((((........(((......)))............))))).).).))..................))))) { 13.20 MEA=92.14}
-
-Alifold.out
- 6 89 9 99.2% 0.023 CG:29 GC:14 UA:9
- 4 91 11 99.1% 0.028 CG:20 GC:11 UG:2 UA:17
- 3 92 18 96.9% 0.090 CG:5 GC:2 GU:1 UG:4 AU:6 UA:25
- 35 46 3 93.3% 0.195 CG:31 GC:16 UG:2 AU:5 UA:4
- 36 45 10 93.6% 0.185 CG:16 GC:6 GU:1 UG:2 AU:8 UA:18
- .
- .
- .
- </pre>
+ <strong>Running RNAalifold from Jalview</strong><br />
+ <p>
+ Jalview supports access to RNAalifold services provided by JABA 2.1
+ servers. To enable RNAalifold predictions for an RNA alignment, go to
+ <strong>Webservices→Secondary Structure Prediction</strong> and
+ select <strong>RNAalifold prediction</strong> to run with current
+ defaults, and <strong>Change settings ...</strong> to adjust
+ prediction parameters. The RNA secondary structure prediction for the
+ alignment will be shown as alignment annotation, and any edits will
+ trigger the prediction to be recalculated.
+ <p>
+ <Strong>RNAalifold prediction parameters</Strong> <br /> JABAWS and
+ Jalview only provide access to a selection of the RNAalifold
+ arguments. For a full description, see the documentation at <a
+ href="http://www.tbi.univie.ac.at/RNA/RNAalifold.html">http://www.tbi.univie.ac.at/RNA/RNAalifold.html</a>.